BamQC report ----------------------------------- >>>>>>> Input bam file = results/1X_low_error_no_variance/alignment/1X_low_error_no_variance.sorted.bam outfile = results/1X_low_error_no_variance/qualimap/genome_results.txt >>>>>>> Reference number of bases = 2,410,976,875 bp number of contigs = 3268 >>>>>>> Globals number of windows = 3667 number of reads = 16,073,088 number of mapped reads = 16,073,088 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,036,544 number of mapped paired reads (second in pair) = 8,036,544 number of mapped paired reads (both in pair) = 16,073,088 number of mapped paired reads (singletons) = 0 number of mapped bases = 2,410,956,923 bp number of sequenced bases = 2,410,956,893 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,305 duplication rate = 0.34% >>>>>>> Insert size mean insert size = 353.1726 std insert size = 6,484.0659 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 32.4529 >>>>>>> ACTG content number of A's = 707,637,937 bp (29.35%) number of C's = 497,978,864 bp (20.65%) number of T's = 707,520,560 bp (29.35%) number of G's = 497,815,248 bp (20.65%) number of N's = 4,284 bp (0%) GC percentage = 41.3% >>>>>>> Mismatches and indels general error rate = 0.001 number of mismatches = 2,411,437 number of insertions = 5 mapped reads with insertion percentage = 0% number of deletions = 14 mapped reads with deletion percentage = 0% homopolymer indels = 52.63% >>>>>>> Coverage mean coverageData = 1X std coverageData = 1.0195X There is a 62.42% of reference with a coverageData >= 1X There is a 26.51% of reference with a coverageData >= 2X There is a 8.39% of reference with a coverageData >= 3X There is a 2.12% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_006583.3 122678785 122755852 1.0006282015264498 1.0170788885981918 NC_006584.3 85426708 85683684 1.0030081458833695 1.0195030189742742 NC_006585.3 91889043 91957931 1.000749686771686 1.0154348125751844 NC_006586.3 88276631 88329226 1.0005957975446527 1.016983432563446 NC_006587.3 88915250 88942900 1.000310970277877 1.0167546249865753 NC_006588.3 77573801 77603614 1.0003843178961929 1.017565260516697 NC_006589.3 80974532 80984251 1.0001200253926754 1.0164202013326604 NC_006590.3 74330416 74329071 0.9999819051194332 1.0173269398011902 NC_006591.3 61074082 61180018 1.001734549198791 1.0201987535062078 NC_006592.3 69331447 69331348 0.9999985720765355 1.0173051447184573 NC_006593.3 74389097 74417541 1.0003823678623227 1.016501583589756 NC_006594.3 72498081 72502063 1.0000549255917546 1.0176058375680717 NC_006595.3 63241923 63259976 1.0002854593779509 1.017138915982697 NC_006596.3 60966679 60984517 1.0002925860534408 1.0177396078267735 NC_006597.3 64190966 64188463 0.9999610069740966 1.01824407180686 NC_006598.3 59632846 59728985 1.001612181984405 1.0204118989400104 NC_006599.3 64289059 64347615 1.0009108237219648 1.0172625929374923 NC_006600.3 55844845 55876075 1.0005592279824576 1.017834211679009 NC_006601.3 53741614 53748547 1.0001290061738748 1.0159944012756583 NC_006602.3 58134056 58136845 1.0000479753210407 1.0191243399104835 NC_006603.3 50858623 50846628 0.9997641501225859 1.0157940995121906 NC_006604.3 61439934 61444384 1.0000724284632208 1.01310675315208 NC_006605.3 52294480 52275818 0.9996431363310239 1.013192500439568 NC_006606.3 47698779 47712834 1.0002946616306467 1.0170066834450358 NC_006607.3 51628933 51620024 0.9998274417176121 1.0150361607990137 NC_006608.3 38964690 39010990 1.0011882553152611 1.019430037632799 NC_006609.3 45876710 45851899 0.9994591809220844 1.0182298329702009 NC_006610.3 41182112 41189586 1.0001814865638752 1.0183393674070365 NC_006611.3 41845238 41828183 0.9995924267416044 1.0145988619825 NC_006612.3 40214260 40213384 0.999978216682341 1.0180762244032295 NC_006613.3 39895921 39894788 0.9999716011067898 1.0150449652118385 NC_006614.3 38810281 38810644 1.0000093531917484 1.0152577230303872 NC_006615.3 31377067 31386253 1.0002927615892205 1.0162493905845753 NC_006616.3 42124431 42134616 1.0002417836813036 1.0181279423138823 NC_006617.3 26524999 26517840 0.9997301036656024 1.015908262830621 NC_006618.3 30810995 30805742 0.9998295089139445 1.0157523598547076 NC_006619.3 30902991 30899637 0.9998914668162703 1.0183435991961554 NC_006620.3 23914537 23928191 1.0005709497950974 1.0201695626087979 NC_006621.3 123869142 123893397 1.0001958114798277 1.0168048282988498 NW_003726127.1 2660953 2666976 1.0022634747776455 1.0226885972449944 NW_003726128.1 1881673 1897795 1.0085679073887972 1.067435189640811 NW_003726129.1 1415205 1421700 1.0045894411057055 1.0652369374235187 NW_003726130.1 1067467 1067093 0.9996496378810773 1.1025514307867872 NW_003726131.1 866315 870300 1.0045999434385875 1.0172749746846093 NW_003726132.1 881102 895495 1.0163352256605933 1.0626838887665855 NW_003726133.1 822601 829186 1.008005096030761 1.0573140123225833 NW_003726134.1 741967 748500 1.0088049738061127 1.0296261466579282 NW_003726135.1 745551 743088 0.9966964030629696 1.1107739783410384 NW_003726136.1 602611 602700 1.000147690632929 1.0157583769698464 NW_003726137.1 573630 571495 0.9962780886634242 1.0512726385458864 NW_003726138.1 666183 661500 0.9929704000252183 1.1039602836888671 NW_003726139.1 557017 561300 1.0076891728618695 1.0781244996615975 NW_003726140.1 510604 506700 0.9923541531206179 1.008244591872944 NW_003726141.1 497093 498300 1.0024281170726606 1.0370501136338648 NW_003726142.1 492630 496800 1.008464770720419 1.0315612006368355 NW_003726143.1 577062 579600 1.0043981409276646 1.1571373133018892 NW_003726144.1 561270 554100 0.9872253995403282 1.1325661203287272 NW_003726145.1 407330 407100 0.9994353472614342 1.0095751901135666 NW_003726146.1 405216 405900 1.0016879886282872 1.0321555185870575 NW_003726147.1 508668 509693 1.0020150668019219 1.1459048835517813 NW_003726148.1 540093 537595 0.9953748706241332 1.2087141732108568 NW_003726149.1 448434 446390 0.9954419156442197 1.085070871695645 NW_003726150.1 377800 379800 1.0052938062466914 1.0428477985476585 NW_003726151.1 384880 380400 0.9883600083142797 1.0805409432735729 NW_003726152.1 367143 365100 0.9944354107255211 1.0402248968785415 NW_003726153.1 399987 401089 1.00275508954041 1.0667025780394415 NW_003726154.1 376204 373200 0.9920149706010569 1.0449183958047639 NW_003726155.1 416178 418500 1.0055793434540028 1.1247861433016417 NW_003726156.1 365470 365400 0.9998084658111472 1.0612330193521096 NW_003726157.1 322752 326700 1.0122323022010709 1.0387317968359662 NW_003726158.1 320591 326700 1.0190554319990268 1.036679555127822 NW_003726159.1 310270 310200 0.9997743900473781 1.0399596376695437 NW_003726160.1 433650 421800 0.9726738152888273 1.1777954348147355 NW_003726161.1 273228 275400 1.0079494048926172 1.0071492830079742 NW_003726162.1 281659 281087 0.9979691754923506 1.0195662286598037 NW_003726163.1 320442 320400 0.9998689310390024 1.1285514094317088 NW_003726164.1 265648 270300 1.017511895440583 1.0118376747868651 NW_003726165.1 241365 243294 1.0079920452426823 1.0081341815329792 NW_003726166.1 234529 236095 1.0066772126261572 1.0282593014347885 NW_003726167.1 252720 259800 1.0280151946818614 1.0897259204032979 NW_003726168.1 254975 257095 1.0083145406412393 1.1107658869750985 NW_003726169.1 226053 227995 1.0085909056725635 1.0050883281885838 NW_003726170.1 223744 227400 1.0163401029748285 1.0458469575354987 NW_003726171.1 227140 231900 1.020956238443251 1.0358295666713224 NW_003726172.1 219672 218700 0.995575221238938 1.0294334090038786 NW_003726173.1 214597 213300 0.9939561130863899 1.005446940464808 NW_003726174.1 386314 388200 1.0048820389631232 1.3800829169101647 NW_003726175.1 204342 207300 1.0144757318612914 0.9995084990398566 NW_003726176.1 201724 202800 1.0053340207412107 1.0585098410444207 NW_003726177.1 216332 213900 0.988758020080247 1.0680371966886302 NW_003726178.1 200877 202500 1.0080795710808106 0.9956517891226586 NW_003726179.1 310654 302400 0.9734302471559999 1.2381933131509395 NW_003726180.1 200932 200400 0.9973523381044334 1.0091418955216722 NW_003726181.1 201410 202200 1.0039223474504742 1.0465101353122324 NW_003726182.1 292533 289800 0.9906574642860806 1.2137683781049449 NW_003726183.1 192561 193500 1.004876376836431 0.9990788833217196 NW_003726184.1 210134 212246 1.0100507295344876 1.0740182711404944 NW_003726185.1 197844 200995 1.0159266897151291 1.0690671571259776 NW_003726186.1 196813 204000 1.0365168967497065 1.0787522547986916 NW_003726187.1 180359 184500 1.0229597635826324 1.0470655696721674 NW_003726188.1 210247 200095 0.9517139364652052 1.0809501814853317 NW_003726189.1 177735 185693 1.044774523869806 1.0186371542984103 NW_003726190.1 172100 180595 1.0493608367228355 1.0776092064980425 NW_003726191.1 166866 171900 1.0301679191686743 1.0207657032222737 NW_003726192.1 164926 170700 1.0350096406873386 1.0572937917058554 NW_003726193.1 157598 158700 1.0069924745237884 1.0739609577706668 NW_003726194.1 143980 144000 1.0001389081816918 1.0099518596785448 NW_003726195.1 141074 139800 0.9909692785346698 1.0267779206542622 NW_003726196.1 139526 137100 0.9826125596662988 0.9940328324293547 NW_003726197.1 142260 147600 1.037536904259806 1.0330934661188556 NW_003726198.1 138160 140400 1.0162130862767806 1.0542867614287053 NW_003726199.1 142296 145200 1.0204081632653061 1.0650562658496907 NW_003726200.1 133119 132300 0.9938476100331283 1.0390983435040406 NW_003726201.1 129748 129600 0.9988593273114036 1.0164955389890376 NW_003726202.1 125962 129000 1.0241183849097346 1.0147634748778693 NW_003726203.1 127429 126894 0.9958015836269609 1.0028514613763428 NW_003726204.1 128261 123900 0.9659990176281177 0.9919123197642022 NW_003726205.1 131872 131400 0.9964207716573648 1.0488996217448399 NW_003726206.1 133432 137400 1.0297379938845255 1.0996977263484216 NW_003726207.1 119670 123300 1.0303334168964653 1.085297913446554 NW_003726208.1 144750 135000 0.9326424870466321 1.0840634369800153 NW_003726209.1 120779 119400 0.9885824522474933 1.036789447023792 NW_003726210.1 115952 112800 0.9728163377949496 1.025160891198035 NW_003726211.1 118237 109500 0.9261060412561212 0.9692419874388208 NW_003726212.1 111908 112500 1.0052900596918897 1.0392916542985209 NW_003726213.1 117332 123589 1.0533273105376197 1.076289694986386 NW_003726214.1 111759 111895 1.0012169042314265 1.003522970963501 NW_003726215.1 108801 113100 1.0395125044806572 1.0603568844037987 NW_003726216.1 112014 114300 1.0204081632653061 1.127012346012292 NW_003726217.1 106428 109800 1.0316833915886796 1.0360018906104709 NW_003726218.1 104912 102000 0.9722434039957297 0.9882409353676439 NW_003726219.1 104646 105600 1.0091164497448541 1.0108980485025818 NW_003726220.1 103248 103800 1.005346350534635 1.0479138508728487 NW_003726221.1 129482 123288 0.9521632350442533 1.138572680059804 NW_003726222.1 118473 117900 0.9951634549644223 1.1087736864311182 NW_003726223.1 99993 100200 1.0020701449101437 1.0179382342153394 NW_003726224.1 109585 111900 1.0211251539900534 1.0206075542499482 NW_003726225.1 124049 118200 0.9528492773017114 1.085578000952036 NW_003726226.1 99658 96295 0.9662545907001947 1.04311860863547 NW_003726227.1 101741 101393 0.9965795500339096 1.0398381137145951 NW_003726228.1 97365 96600 0.9921429671853336 1.0434261563655454 NW_003726229.1 94395 94500 1.0011123470522802 0.9894131215831239 NW_003726230.1 102992 99300 0.9641525555382943 1.0326334601441294 NW_003726231.1 95509 94500 0.9894355505763854 1.0749987939546066 NW_003726232.1 92047 93600 1.0168718154855672 1.0451828160035805 NW_003726233.1 87753 87000 0.991419096783016 0.9903672581217815 NW_003726234.1 96536 94493 0.9788369105825806 1.0489577978920397 NW_003726235.1 86544 86700 1.0018025513033832 1.0272770319691338 NW_003726236.1 85476 85500 1.0002807805699845 0.9685734883024317 NW_003726237.1 110512 106200 0.9609816128565224 1.152921930173995 NW_003726238.1 83291 82200 0.9869013458837089 1.0373712889459603 NW_003726239.1 82459 85500 1.0368789337731479 0.9765986409458225 NW_003726240.1 81605 85200 1.0440536731817904 0.989229585910286 NW_003726241.1 82380 84300 1.0233066278222869 1.0507702539870505 NW_003726242.1 102198 102893 1.0068005244721032 1.195585211058999 NW_003726243.1 82108 81900 0.9974667511082964 1.0762761516945216 NW_003726244.1 87041 89700 1.0305488218196022 1.0981610878526427 NW_003726245.1 79722 76500 0.9595845563332581 1.004504177462267 NW_003726246.1 230124 226800 0.9855556134953329 1.7213601356894477 NW_003726247.1 78357 78600 1.0031011907040852 1.0393697736028287 NW_003726248.1 256406 251393 0.9804489754529925 1.7983911008675355 NW_003726249.1 78050 80400 1.0301089045483665 0.988617111622514 NW_003726250.1 81930 83100 1.014280483339436 1.0710354576188332 NW_003726251.1 77100 78300 1.0155642023346303 1.000034519230401 NW_003726252.1 77130 76800 0.9957215091404122 0.943486669639029 NW_003726253.1 79078 80400 1.0167176711601205 1.036523507352094 NW_003726254.1 90550 84900 0.9376035339591386 1.088981306895713 NW_003726255.1 82767 81594 0.9858276849468991 1.127737383546978 NW_003726256.1 89070 85200 0.9565510272819131 1.0909975498166165 NW_003726257.1 97802 96600 0.9877098627839922 1.1679448113944444 NW_003726258.1 79712 79800 1.001103974307507 1.0345175693980637 NW_003726259.1 79581 78000 0.980133448938817 1.021302062590636 NW_003726260.1 73720 74400 1.0092240911557244 0.9910870267272829 NW_003726261.1 97799 95098 0.9723821306966329 1.1041732665633561 NW_003726262.1 73171 72900 0.9962963469133946 0.9740450729318963 NW_003726263.1 104732 102900 0.9825077340258946 1.2041616549711673 NW_003726264.1 78935 72000 0.9121429023880407 1.0052482223048014 NW_003726265.1 72992 75300 1.031619903551074 1.07442406591326 NW_003726266.1 68721 71700 1.0433491945693456 1.0287684097946996 NW_003726267.1 73611 73494 0.9984105636385866 1.074583539201096 NW_003726268.1 68272 67800 0.993086477618936 1.0144169396575573 NW_003726269.1 79297 79200 0.9987767506967477 1.1156833111829194 NW_003726270.1 84443 81300 0.962779626493611 1.0463372078820634 NW_003726271.1 80679 76500 0.9482021343844123 1.0809094362069063 NW_003726272.1 68834 66600 0.9675451085219514 0.989804020745201 NW_003726273.1 67496 67500 1.000059262771127 1.1301334471801543 NW_003726274.1 66523 66300 0.9966477759571878 0.9927374269090293 NW_003726275.1 67057 67200 1.0021325141297701 1.0215674950276703 NW_003726276.1 66195 68693 1.03773698919858 1.0962014976307228 NW_003726277.1 87584 82486 0.9417930215564486 1.172502967230648 NW_003726278.1 84679 84594 0.9989962092136185 1.1244070445379752 NW_003726279.1 65840 66900 1.0160996354799514 0.9921696341983983 NW_003726280.1 65696 68700 1.045725767169995 0.9767499298832802 NW_003726281.1 66021 65100 0.986049893215795 0.9874490840888711 NW_003726282.1 67300 68100 1.011887072808321 1.038847875531154 NW_003726283.1 88153 85200 0.9665014236611347 1.1593808184372538 NW_003726284.1 92437 88497 0.9573763752609885 1.2147517913489054 NW_003726285.1 70351 70200 0.9978536197068982 1.089456408608826 NW_003726286.1 64646 67195 1.039430127154039 1.052996363064217 NW_003726287.1 69126 68700 0.9938373405086364 1.0306571049752686 NW_003726288.1 227674 212393 0.9328821033583106 1.800841176326669 NW_003726289.1 64123 63000 0.9824867832135116 1.0451448489895308 NW_003726290.1 61944 60900 0.9831460674157303 1.0049149885879627 NW_003726291.1 62414 62700 1.0045823052520269 1.0276147509978568 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